The reenactment shows debris covering the entire vault floor and the larger chunks blown several feet into the middle of the vault floor. When the CSIs are in the vault, the large debris is piled next to the hole in the wall and there is only a minor amount of dust and small debris on the floor leaving it mostly clean.
Horatio drops an orange onto the box of oranges. The falling orange lands on the packets of white powder which were under a wooden board. Between picking up the orange and letting it fall, there is no time to remove the wooden box floor. When Horatio picks up the orange, the wooden floor is in place.
Towards the end of the episode, Detective Tripp searches a "Gun Registration" database to find the owner of the 9mm discovered under the concrete. The state of Florida does not register guns, nor do they have a database of gun serial numbers.
Even though Florida may not register guns, the NCIC (National Crime Information Center) holds records of weapons in association with crimes or that have been stolen. They could have run a serial number through it, not just a Florida database.
When Ryan Wolfe uses the Ground Penetrating Radar to locate the gun under the concrete pad, he says he has a reflection at 18 inches deep. But the concrete pad was only about 3 inches thick and the gun was right underneath it, so the reflection should have only been about 4 inches deep.